Contacts of the helix formed by residues 473 - 482 (chain D) in PDB entry 1ZQ1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 473 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472D LEU* 1.3 78.4 - - - +
474D ARG* 1.3 78.2 + - - +
475D SER* 3.0 23.1 + - - -
476D LEU* 3.6 27.5 - - + +
477D ALA* 2.8 27.2 + - - +
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Residues in contact with ARG 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D VAL* 5.9 4.9 - - + +
464D GLU* 4.5 14.3 + - - -
467D VAL* 3.7 29.2 - - + +
472D LEU 3.5 1.8 + - - -
473D ASP* 1.3 74.7 + - - +
475D SER* 1.3 67.9 + - - +
477D ALA* 3.7 1.1 - - + +
478D GLN* 3.0 33.1 + - - +
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Residues in contact with SER 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D ASP* 3.0 19.4 + - - -
474D ARG* 1.3 80.3 - - - +
476D LEU* 1.3 63.2 + - - +
478D GLN* 3.8 3.4 - - - +
479D THR* 3.0 34.2 + - - -
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Residues in contact with LEU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D LEU* 4.6 6.7 - - + -
473D ASP* 3.3 30.1 + - + +
474D ARG 3.3 0.4 - - - -
475D SER* 1.3 83.7 - - - +
477D ALA* 1.3 59.6 + - - +
479D THR* 3.7 4.3 - - + -
480D LEU* 2.8 33.8 + - - +
501D LEU* 5.3 6.1 - - + -
504D SER* 3.8 28.5 - - - +
505D ILE* 4.1 13.7 - - + +
508D VAL* 4.2 13.6 - - + +
509D VAL* 3.8 26.9 - - + -
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Residues in contact with ALA 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D VAL* 3.7 29.1 - - + +
466D TYR* 4.2 16.7 - - + -
467D VAL* 3.8 13.9 - - + -
472D LEU* 4.7 6.0 - - + +
473D ASP 2.8 21.2 + - - +
474D ARG 3.3 4.7 + - - +
476D LEU* 1.3 74.9 - - - +
478D GLN* 1.3 65.0 + - - +
480D LEU* 3.3 14.3 - - - +
481D VAL* 3.3 14.0 + - - +
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Residues in contact with GLN 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D GLN* 2.7 33.8 + - - +
463D VAL* 3.6 25.1 - - + +
474D ARG* 3.0 24.0 + - + +
475D SER* 3.8 4.0 - - - +
477D ALA* 1.3 71.7 - - - +
479D THR* 1.3 51.4 + - - +
480D LEU 2.8 4.4 + - - -
481D VAL* 2.7 10.8 + - - +
482D ASP* 2.6 71.6 + - - +
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Residues in contact with THR 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D SER* 3.0 19.5 + - - -
476D LEU* 4.2 2.5 - - + -
478D GLN* 1.3 77.2 - - - +
480D LEU* 1.3 60.3 + - - +
481D VAL 3.3 0.2 - - - -
482D ASP* 4.1 7.8 + - - +
483D ASP* 3.0 38.3 + - + +
485D ARG* 5.1 0.3 - - - +
508D VAL* 3.5 33.4 - - + +
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Residues in contact with LEU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D TYR* 4.1 11.4 - - + -
472D LEU* 4.5 3.6 - - + -
476D LEU 2.8 19.6 + - - +
477D ALA* 3.3 6.3 - - - +
478D GLN 2.8 0.6 + - - -
479D THR* 1.3 78.3 - - - +
481D VAL* 1.3 59.9 + - + +
485D ARG* 3.0 31.1 + - + +
486D ASP 2.9 20.1 + - - -
489D PHE* 3.1 62.8 - - + -
504D SER* 4.3 15.9 - - - -
507D VAL* 4.0 19.7 - - + -
508D VAL* 4.7 5.6 - - + +
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Residues in contact with VAL 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D PRO* 4.2 31.2 - - + +
462D LYS* 4.6 3.8 - - + -
463D VAL* 3.6 30.1 - - + +
466D TYR* 4.0 19.1 - - + -
477D ALA 3.6 5.6 - - - +
478D GLN* 2.7 12.1 + - - +
480D LEU* 1.3 73.1 - - - +
482D ASP* 1.3 54.3 + - - +
483D ASP 2.7 5.9 + - - -
484D GLU* 2.7 26.5 + - - -
486D ASP* 3.9 26.2 - - + -
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Residues in contact with ASP 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D GLN* 5.7 1.4 + - - -
478D GLN* 2.6 54.2 + - - +
479D THR* 4.3 5.1 + - - -
481D VAL* 1.3 73.3 - - - +
483D ASP* 1.3 63.1 + - - +
484D GLU 3.5 1.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il